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Merge pull request #56 from broadinstitute/md_relax_boundquals_checks 

Relax bounds checking in QualityUtils.boundQual
This commit is contained in:
Eric Banks 2013-02-22 07:08:41 -08:00
parent c8a01e6569 182c32a2b7
commit 34ee953798
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
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@ -375,13 +375,14 @@ public class QualityUtils {
* WARNING -- because this function takes a byte for maxQual, you must be careful in converting
* integers to byte. The appropriate way to do this is ((byte)(myInt & 0xFF))
*
* @param qual the uncapped quality score as an integer
* @param qual the uncapped quality score as an integer. Can be < 0 (which may indicate an error in the
* client code), which will be brought back to 1, but this isn't an error, as some
* routines may use this functionality (BaseRecalibrator, for example)
* @param maxQual the maximum quality score, must be less < 255
* @return the bounded quality score
*/
@Ensures("(result & 0xFF) >= 1 && (result & 0xFF) <= (maxQual & 0xFF)")
public static byte boundQual(final int qual, final byte maxQual) {
if ( qual < 0 ) throw new IllegalArgumentException("qual must be >= 0 " + qual);
return (byte) (Math.max(Math.min(qual, maxQual & 0xFF), 1) & 0xFF);
}
}